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human PKM2 with L-serine and FBP bound.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3H6O PDB ENTRY 3H6O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 PROTEIN SOLUTION 10 MG/ML, 25 MM TRIS/HCL PH 7.5, 0.1 M KCL, 5 MM MGCL2, 10% (V/V) GLYCEROL WAS MIXED IN A (1:1) RATIO WITH RESERVOIR SOLUTION CONTAINING 0.1 M KCL, 0.2 M AMMONIUM TARTRATE, 24% (W/V) PEG3350
Crystal Properties Matthews coefficient Solvent content 2.28 46.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.611 α = 90 b = 151.098 β = 102.01 c = 91.791 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.3 89.78 98 0.08 11.5 3.7 93236 2 47.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.36 97.9 0.83 1.6 3.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3H6O 2.3 78.85 93185 4702 97.91 0.1762 0.1735 0.1787 0.2262 0.2324 RANDOM 58.69
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 8.1671 12.2442 -7.3352 -0.8318
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 18.04 t_omega_torsion 5.88 t_angle_deg 1.09 t_bond_d 0.012 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 18.04 t_omega_torsion 5.88 t_angle_deg 1.09 t_bond_d 0.012 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15595 Nucleic Acid Atoms Solvent Atoms 1243 Heterogen Atoms 110
Software Software Software Name Purpose BUSTER refinement XDS data reduction SCALA data scaling CSEARCH phasing